A Science Driven Life

An un-edited blog about science, discovery, technology, travel and the occasional whiskey


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Two big moves this week!  First I’m moving my home this weekend, and more relevant, I’m moving my blog.

Those interested to continue following, please head over to http://www.scienceandwine.com!

New posts coming, hope to see you soon!


Written by Michael Mohammadi

July 29, 2014 at 12:53

Posted in Uncategorized

Dendrite Pruning and Optical Methods in Neuroscience

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Screen Shot 2014-04-03 at 11.07.57 AMAs always this is meant to be a brief overview of a paper (and the methods used in neuroscience) I happened to have found interesting- for more details please refer to the manuscript itself.

I enjoyed reading a relatively recent paper published in Science from group in Japan (Kazuo Emoto, The University of Tokyo)  that suggests a role for Ca2+ signaling in dendritic pruning, a house-cleaning function in neurons that has been shown to be very important in learning and memory, as well as experience and some forms of cognitive deficits (such as autism and neurodegeneration).

Dendrites are highly branched areas of the cell that act as antennae receive information from neighboring cell.  Pruning refers to a highly complex, regulated, activity dependent process in which connections that are non-essential to the formation of the developing brain are cleaved.

In pruning, our neurons clean house.  Unnecessary connections formed during development are trashed as a way to reduce clutter and improve accuracy and efficiency of signaling.  Many of the basic mechanisms behind how pruning works have been identified.  Specific cascades of enzymes (caspases) as well as a key self-destruction pathway (proteosome-ubiquitin) work together to rid individual neurons of unnecessary connections.  While a lot is known about the processes that regulate the pruning, very little is known about the signaling that tells which dendritic arbors (branches of dendrites) are to be pruned and which of those is to be kept as a part of the neural network.

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Written by Michael Mohammadi

April 15, 2014 at 15:37

What is the current technical limitation in your scientific field?

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Lavoisier conducting an experiment related combustion generated by amplified sun light.As a neuroscientist working for a technology company I spend a lot of time seeing new applications. These can range from new imaging probes, to new optogenetics tools or transgenic animals, all the way to new camera sensor technologies or super resolution algorithms. I spend a lot of time in labs seeing some really cool research, long before it’s published or presented at a conference. This is an aspect of my job I really love- getting to see where the fields of advanced imaging, electrophysiology, optophysiology, optogenetics, and neuroscience are headed.

The researchers we work with are constantly pushing the barriers of the latest and greatest in technology to better address increasingly complex questions in biology (side note: we also work with astronomers, physical science and chemistry, but I’m heavily focused on biological applications).

My question to my research friends and readers is simply this: what is the current technical limitation(s) in your field and if you could have one single new tool (either a new technology, new probe, new animal model, behavioral test, etc) what would you want?

I’m hoping to get a range of responses to open this up for a bigger question in how can we (academia and industry) work together to form open partnerships that are focused on advancing science. A lot of research money is wasted on overpriced, outdated, and often times the wrong technology for the research question at hand (I blame the sales rep as well as the researcher who doesn’t spend the time to educate her/himself) and an open discussion on how to save researchers time and (all of us taxpayers) money is long overdue.

Written by Michael Mohammadi

April 5, 2014 at 08:42

SDL Book Club: April 2014: Mirroring People – Marco Iacoboni

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Screen Shot 2014-04-04 at 7.28.31 PMApril 2014:  Mirroring People: The New Science of How We Connect with Others – Marco Iacoboni

Please have this book ready by April 30, 2014!

What accounts for the remarkable ability to get inside another person’s head—to know what they’re thinking and feeling? “Mind reading” is the very heart of what it means to be human, creating a bridge between self and others that is fundamental to the development of culture and society. But until recently, scientists didn’t understand what in the brain makes it possible.

This has all changed in the last decade. Marco Iacoboni, a leading neuroscientist whose work has been covered in The New York Times, the Los Angeles Times, and The Wall Street Journal, explains the groundbreaking research into mirror neurons, the “smart cells” in our brain that allow us to understand others. From imitation to morality, from learning to addiction, from political affiliations to consumer choices, mirror neurons seem to have properties that are relevant to all these aspects of social cognition. As The New York Times reports: “The discovery is shaking up numerous scientific disciplines, shifting the understanding of culture, empathy, philosophy, language, imitation, autism and psychotherapy.”
Mirroring People is the first book for the general reader on this revolutionary new science.

Written by Michael Mohammadi

April 4, 2014 at 18:29

Posted in Book Club, Neuroscience

Brief review: Simultaneous two-color optogenetics using novel probes (Klapoetke et al., 2014)

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Cartoon structure of rhodopsin – Wikipedia Commons

To catch up on the field of optogenetics, here is a primer and here is an update on some new stuff.  Also refer to the literature (Mattis et al., 2011; Fenno et al., 2011).  This post assumes a working understanding of Optogenetics, Electrophysiology and some genetics.

A recent paper out of MIT (Ed Boyden lab) identifies two new probes in the ever growing quest to find improve optogenetic tools that will allow for greater spectral separation of activation/excitation wavelengths.  Some of the major challenges for optogenetics research are:

  • genetically expressing opsins, or other light sensitive molecules in model organisms/specific cells
  • finding the right probe that addresses a specific need (i.e. high frequency stimulation, or activate a specific Gi/o pathway)
  • delivering light of a specific wavelength to a particular target in tissue and/or specific cell types
  • spectrally separating a single probe (i.e. ChR2 activated at 470nm) from an imaging probe (i.e. GCamp3, or even the new RCamp which can be activated by blue light)
  • finding two or more probes to express that will not “cross-talk”- such that excitation wavelength of probe 1 will not activate probe 2

Optogenetics allows for very precise control of cell excitability and/or signaling pathways and researchers continue to push the limit of the existing tools and pharmacological agents.  For instance, if studying the interaction of interneurons in the hippocampus area CA1 it would be beneficial to be able to simultaneously activate CCK interneurons while optically inhibiting PV interneurons, or vice versa.  There are currently methods of blocking one versus the other (machR agonist carbachol for instance activates CCK only) but to rapidly be able to control the activity of these neurons would be of great interest in studying the details of synaptic transmission of individual or small groups of neurons (worth noting is these types of on/off, two wavelength probes exist for other applications such as PIF-2.

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Written by Michael Mohammadi

March 31, 2014 at 05:17

Targeting Light: Two recent papers that use active illumination!

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Screen Shot 2014-03-20 at 5.02.10 PMIn my day job I get to travel quite a bit and visit labs around the world who use methods in microscopy in imaging.  These labs range from neuroscience to developmental biology and everything in between, and many of these labs have very specific needs when it comes to light delivery.  The applications I most often work with can involve from high power lasers for ablation and thrombosis, or FRAP or photoconversion.  I’m very focused on optogenetics and uncaging, as well as any type of imaging, especially the use of genetically encoded indicators (for voltage, ions, temperature, pH, etc).  

While many people tend to use a simple configuration for single spot/point illumination, or full field illumination (and we provide these tools as well) where we are unique is in systems that allow for “targeted” or “active illumination.”  There are many methods for targeting light (possibly a good topic for an upcoming review) but the two of the main methods used are either using a galvo-mirror system (very fast mirrors that move a single spot of light in X-Y to create regions with the ability to target to a diffraction limited spot) or a digital micromirror device, or DMD.  

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Written by Michael Mohammadi

March 20, 2014 at 16:04

SDL Book Club March 2014: Braintrust: What Neuroscience Tells Us about Morality

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Screen Shot 2014-03-01 at 2.22.35 PM

March 2014Braintrust: What Neuroscience Tells Us about Morality – By Patricia Churchland

Please have this read by March 24, 2014 for a discussion within a week of that date.

From Wikipedia:  “Particia Churchland is a is a Canadian-American philosopher noted for her contributions to neurophilosophy and the philosophy of mind. She is UC President’s Professor of Philosophy Emerita at the University of California, San Diego (UCSD), where she has taught since 1984. She has also held an adjunct professorship at the Salk Institute for Biological Studies since 1989. Educated at the University of British Columbia, the University of Pittsburgh, and the University of Oxford, she taught philosophy at the University of Manitoba from 1969 to 1984 and is married to the philosopher Paul Churchland.”

Patricia Churchland previously wrote a book called Neurophilosophy in which she lays the foundation for the study of philosophy based on basic neuroscience and does a nice job giving an overview of neuropsychology and develops a template for studying philosophy from a basic resaerch persepctive.  In Braintrust, Churchland attempts to describe what we know about morality and moral behavior through social sciences and the underlying neural mechanisms (mostly from preclinical/animal research).  This should be a fun read for us all and I look forward to discussing it with you all next month!

Written by Michael Mohammadi

March 1, 2014 at 14:28

Posted in Book Club, Neuroscience